Plasma Functionalization of Silica Bilayer Polymorphs

Ultrathin silica films are considered suitable two-dimensional model systems for the study of fundamental chemical and physical properties of all-silica zeolites and their derivatives, as well as novel supports for the stabilization of single atoms. In the present work, we report the creation of a new model catalytic support based on the surface functionalization of different silica bilayer (BL) polymorphs with well-defined atomic structures. The functionalization is carried out by means of in situ H-plasma treatments at room temperature. Low energy electron diffraction and microscopy data indicate that the atomic structure of the films remains unchanged upon treatment. Comparing the experimental results (photoemission and infrared absorption spectra) with density functional theory simulations shows that H2 is added via the heterolytic dissociation of an interlayer Si–O–Si siloxane bond and the subsequent formation of a hydroxyl and a hydride group in the top and bottom layers of the silica film, respectively. Functionalization of the silica films constitutes the first step into the development of a new type of model system of single-atom catalysts where metal atoms with different affinities for the functional groups can be anchored in the SiO2 matrix in well-established positions. In this way, synergistic and confinement effects between the active centers can be studied in a controlled manner.

S-2   Fitting of all spectra was performed using a least squares curve-fitting protocol available in the WinSpec software. All lines were fitted using a Lorentzian line shape, unless stated otherwise. For the core-line analysis, a Shirley function was used to account for the background. A Gaussian broadening accounting for the instrumental contribution to the full width at half maximum (FWHM) and the line shape was estimated in a first step for the pristine sample and then maintained constant for all subsequent fittings corresponding to the different plasma exposure times. A doublet separation (spin-orbit splitting) of (0.63±0.02) eV and an intensity ratio of (1.96±0.05) were used for the Si 2p1/2 and 2p3/2 lines. The results obtained were validated by comparing the obtained FWHM of the different components to those reported in the literature.

Geometries
The system under study is a repeated slab, consisting of five layers of 16 ruthenium atoms terminated with a (0001) surface, covered by chemically adsorbed oxygen atoms (4 oxygen atoms per unit cell, corresponding to a 1O-coverage in the nomenclature of reference 2 ). A pristine silica bilayer is bound to the Ru-substrate on one side by van der Waals forces, while some (potential) defects may form covalent bridges to the surface (vide infra). The pristine bilayer is shown in Figure S9.
In this study we focus on pure hydrogenation defects. Experimentally, both deuterium and hydrogen are used for the functionalization of the bilayer, depending on the experiment. For the calculation of the IR spectra, all hydrogen atoms were replaced by deuterium atoms in the functionalized structure.
The first set of geometries considered results from the hydrogenation of a single Si-O-Si bond in the bilayer, consequently both hydrogen atoms must be located on neighbouring atoms. All considered structures are shown in Fig. S10. We refer to this set of structures as bondsaturating single D2 type defects.
A second set of structures was obtained by adapting those in Ref. 3 In this study, the authors focused on defects of the silica bilayer that can be formed by the addition of two water molecules instead of hydrogen molecules. Consequently, we adapted the structures by replacing two OH groups with hydrogen atoms. Within this study, three types of structures were distinguished: S-9  vicinal I: here all defects (two OH groups and two H atoms) are evenly distributed amongst four directly neighbouring Si atoms. The structures are shown in Fig. S11  geminal: here two defects are located on the same Si atom, while the other two are distributed amongst the remain two neighbouring Si atoms. This is equivalent two cleaving two Si-O-Si bonds for the same Si atom. We refer to these two sets (vicinal I and geminal) as double D2 type defects. Representations of the structures are shown in Fig. S12.
 vicinal II: This set of structures is also adapted from Ref. 3 , however in contrast to the other two, these structures feature covalent Si-Ru bonds between the bilayer and the metal substrate, in addition to two H atom defects in the top layer. Since this is equivalent to reacting with a single H2 molecule as for the very first set mentioned, we also refer to these as under single hydrogen type defects. The two corresponding structures are shown in Fig. S13.
All obtained trial defect structures were re-optimized. Note that the numbers used in the nomenclature -1 and 2 -refer to structural isomers of the same type, that include different hydrogen bonding motifs between hydroxyl groups and the interlayer oxygen atoms of the silica bilayer.

Theory
X-Ray photoelectron spectroscopy (XPS) is an established tool to probe atomic species and their chemical environment in a sample. It exploits the fact that tightly bound core electrons, although not directly participating in chemical bonding, are strongly influenced by the effective potential from the valence electrons, which in turn are strongly affected by local changes in geometry and composition. By measuring the ionization potentials (IPs) for the core electron ionization and the shifts in the IPs in a reaction, one can extract information on changes in the local chemical environments of these atoms.
The physical quantity of interest is the binding energy (BE) of an electron, which is obtained as the difference between the ionized and the ground state energy. In a periodic context however, a direct calculation of an ionized system is difficult, especially when handling core states in the context of plane wave basis sets. The simplest approach to cope with this problem is to consider the ionization potential within Koopmans' theorem, i.e. using orbital energies, resulting in the so-called initial state approximation. Core states are then represented using pseudo-orbitals formed in the projector augmented wave (PAW) method, as implemented in VASP. 4 Within this approximation, the absolute BEs are not sufficiently accurate but, due to error compensation, the relative BE shifts are of reasonable quality, in particular for the SiO2 bilayer. 5

Results
The obtained BE shift values (Figs. S14 to S17) for the atoms under consideration exhibit a uniformly negative trend in the range between 0 and -0.8 eV. On close examination, one can find a dependence of the shift value on the H-bonding configuration in the structure. For the single H2 type structures, there is one outlier for the both-bottom type geometry (Fig. S13), likely resulting from the strong interaction of the OH group with the metal interface. In all cases, the hydrogenated silicon atoms show a slightly stronger shift than the hydroxylated species. Although these results are in line with the experimental shifts, they do not allow the identification of any particular candidate structure. In order to characterize distinct features for each structure, we also calculated the IR spectra in order to compare them to the experimental spectra. For all other structures representing the double addition of H2 (D2) molecules, the same trend is observed, with some heterogeneity in the calculated BE shifts reflecting the local interaction of the functional groups via H-bonding.

IR Spectra 3.3.1 Pristine bilayer
The IR spectrum of the pristine, crystalline SiO2 bilayer adsorbed on a (0001) ruthenium surface is shown in Fig. S18. It features the distinctive peak of the bilayer bridging oxygen stretch at 1303cm -3 . Figure S18. The IR absorption spectrum for the pristine bilayer, calculated using the zcomponent of the dipole-moment derivative only.

Defective bilayer
The following figures show the IR spectra calculated for the structures discussed above, where all hydrogen atoms have been replaced with deuterium atoms. For all calculations, the ruthenium atoms were excluded in the calculation of the Hessian matrix and dipole moments, i.e. they act as a rigid support material. The figures are in order of appearance: • Bond-saturating single-D2 -Figure S19  More subtle effects are observed for the structural isomers of the same type, where different locations of the OD groups also influence the position of the Si-D stretching mode. This results, for example, in the "inversion" of the Si-D stretching modes, observed in the vicinal I -crossed case or the splitting of the degenerate Si-D stretching mode in the vicinal I -stacked case.

Bond-saturating single D 2 type defects
The main difference between the bond-saturating single D2 and the other defects is that there is exactly one Si-D group and one OD group per unit cell (rather than two or none). Consequently, there is exactly one peak for the stretching mode of each group in the spectrum. However, for some of the structures (both-bottom, both-top and both-top-flipped), these peaks are extremely weak, as the defects there are oriented parallel to the surface and therefore a virtually zero dipole change occurs along the z-coordinate. Figure S19. The IR absorption spectrum for the different bond-saturating single D2 geometries under consideration with all hydrogen atoms replaced by deuterium atoms, calculated using the z-component of the dipole-moment derivative only).

Vicinal I type defects
The vicinal I type defect consists of two OD and two deuterium terminated silicon atoms, resulting from the interaction with two deuterium molecules on the intralayer oxygen bonds. From the six different geometries under consideration, the so-called same side -1 is different from the crossed and stacked configurations, as it features twice the same defect in one layer, while for the others, the two defect types are always distributed evenly across the top and bottom layer.
This property is also observed in the corresponding infrared spectra (Fig. S20 bottom), where the peaks corresponding to the O-D stretching mode are redshifted considerably between the two isomers same side -1 and same side -2, while for the other structures, they are largely comparable.

Geminal type defects
Similar to the vicinal I type defects, the geminal structures are formed by hydrogenation of two Si-O-Si-intralayer bonds, however in this instance, one of the participating silicon atoms carries both defects. Due to the alignment of the OD-groups on the upper defect with the xyplane, there is almost no change in the z-component of the dipole moment vector when stretching this bond. Consequently, the intensities in the IR spectrum are extremely low. Figure S21. The IR absorption spectrum for the different geminal type defects under consideration with all hydrogen atoms replaced by deuterium atoms, calculated using the zcomponent of the dipole-moment derivatives only). S-20

Vicinal II type defects
For the vicinal II type geometries, the additional bilayer-substrate bonds alter the chemical environment considerably. Additionally, due to the absence of hydroxyl groups in these structures, the corresponding bands are entirely missing in the spectrum (Fig. S22). Figure S22. The IR absorption spectrum for the different Vicinal II geometries under consideration with all hydrogen atoms replaced by deuterium atoms, calculated using the zcomponent of the dipole-moment derivatives only).

Relative energies
In order to analyse the defects from an energetic point of view, we compare DFT total energies for all optimized defect structures considered. Table S1 summarizes the relative electronic stability for both types of defects considered. For the double H2 defects, the geminal type structures are energetically the most preferable. All of them lie within a 0.1 eV (2.3 kcal/mol) range with respect to the global minimum. The vicinal I structures are somewhat higher, which does not render them inaccessible, as kinetic hinderance may still prevent these structures from finding lower configurations. Nonetheless, the energy difference for most of the vicinal II type structures is above the geminal type by about 0.3 eV (7 kcal/mol) or more. As for the single H2 defects, the energetically lowest structures are "OH top" and "both topflipped". The "OH bottom" and "both bottom" structures are somewhat higher in energy. The "both-top" and especially the vicinal II type structures are substantially higher, which suggests that their presence is most unlikely.

Kinetic analysis of the hydroxylation process
Based on the simple model that one formed pair of Si-OH and Si-H blocks the three involved pores for further hydroxylation one can describe the surface as an arrangement of dense packed unit cells as shown in Fig. S23. With the landing rate being = .
Comparing eq. S3 with eq. S4, one finds the fraction of the flux of incoming H2 + used for the hydroxylation: = ≈ 0.35 = 35% (eq. S5) That means during the initial process the incoming plasma activate H2 + are nearly completely used for the hydroxylation (and hydrogenation) of the silica, exhibiting a high reactivity of the species. The rest contributes either to the removal of the interfacial oxygen at the Ru(0001) surface or does not react with the surface.